A. General Information
The roof of your home is your first line of defense against the elements. Most roof problems are caused by water. Finding the source of a leak can be tough, but the laws of nature work in your favor.
B. Tracing Leaks
Water usually follows a winding path, but eventually it always runs downhill. If you have an unfinished attic, examine the underside of your roof with a strong flashlight on a rainy day. If you find wetness, discoloration, or other signs of moisture, trace the trail up to where the water is making its entrance. Water that flows down toward a wall can be temporarily diverted to minimize the damage.
Nail a small block of wood in the path of the water and place a bucket underneath to catch the drip.
Then, on a dry day, drive a nail through the underside of the decking in order to locate and repair the hole.
C. Minor Roofing Repairs
If there are no obvious signs of wetness, check the insulation between the rafters. Wearing a respirator, long sleeves, and heavy gloves, examine the insulation for mold, discoloration, and dampness. Remove insulation until you find the leak. If the leak is finding its way to a finished ceiling, take steps to minimize damage until the leak can be repaired.
Reduce the accumulation of water behind a ceiling by poking a small hole in the wallboard or plaster and draining the water.
When you find the source of a leak from inside, measure between that spot and a point that will be visible and identifiable from outside the house, like a chimney, vent, pipe, or - if nothing else - the peak of the roof. Then, get up on the roof and use these measurements to locate the leak. While you're there, check for damaged or missing shingles, tiles, or slates; deteriorated flashing; exposed nails; open joints between the roof and siding; damaged chimney masonry; open seams in roofing materials; and missing window or door drip caps.
Choose a dry, moderate day to make minor roof repairs. If shingles appear brittle, warm them slightly with a hair dryer. To reattach a loose shingle, wipe down the building paper and the underside of the shingle.
Let each dry, then apply a liberal coat of roofing cement. Press the shingle down to seat it in the bed of cement. Tack down buckled shingles by cleaning out below the buckled area, filling with roofing cement, and pressing the shingle into the cement. You can also patch cracks and splits with roofing cement. Check the joints around flashing, which are common places for roof leaks to occur.
Seal gaps by cleaning out and replacing any failed roofing cement.
D. Replace Asphalt Shingles
Replace asphalt shingles by pulling out damaged shingles, starting with the uppermost shingle in the damaged area. Be careful not to damage surrounding shingles that still are in good condition. Exposed nail heads can puncture new shingles, so remove all the old nails in and above the repair area. Patch damaged building paper with roofing cement. Install the replacement shingles, beginning with the lowest shingle in the repair area. Nail above the tab slots with 1" roofing nails. Install all but the top shingle with nails, then apply roofing cement to the underside of the top shingle, above the seal line. Slip the last shingle into place, under the overlapping shingle. Lift the shingles immediately above the repair area, and nail the top replacement shingles into place.
E. Flashing Protects the Joints
Flashing protects the joints surrounding roof elements and the seams between roof areas by carrying water off the roof's surface. When repairing valley flashing, the damaged flashing is not removed, but is patched over with pieces of new material. Measure the damaged area and mark an outline for the patch.
The patch should be wide enough to slip under the shingles on both sides of the repair area, and tapered to a point at one end. Cut the patch with aviation snips. Using a trowel or flat pry bar, carefully break the seal between the damaged flashing and the surrounding shingles. Scrub the damaged flashing with a wire brush, and wipe it clean.
Apply a heavy bead of roofing cement to the back of the patch. Cut a slit in the old flashing. Insert the tapered end of the patch into the slit in the old flashing, and slip the side edges under the shingles on each side. Rest the square end of the patch on top of the old flashing, and press it firmly to seal the roofing cement joint. Add roofing cement to the exposed seams and at the shingle joints. Using a trowel, feather out the cement to create a smooth path for water flow. Make sure all of the seams are covered.
F. Removing Shingles
Removing shingles, commonly referred to in the roofing trade as the tear-off, can be done pretty quickly. If you can't reshingle your whole roof in one day, tear off one section at a time.
Remove the ridge cap with a flat pry bar. Then work downward, tearing off the building paper and old shingles with a roofing shovel or pitchfork. Unless flashing is in exceptional condition, remove it by slicing through the roofing cement that attaches it to the shingles. You might be able to salvage flashing pieces and reuse them.
After removing shingles, building paper, and flashing from the entire tear-off section, pry out any remaining nails and sweep the roof with a broom. At night, cover any unshingled sections using tarps weighted down with shingle bundles.
G. Replacing Sheathing
If you find a soft spot while inspecting your roof after the tear-off,
or see a portion of damaged sheathing, you have to replace it. Check under the sheathing for wiring. Use a reciprocating saw to cut to the rafters in an area that extends well beyond the damaged area. Pry out the damaged sections. Attach 2 x 4 nailing strips to the inside edge of the rafters with 3" deck screws.
Use exterior grade plywood to make a patch. Measure the area and cut the patch, allowing for a 1/8" gap on all sides for expansion. Attach the patch to the rafters and nailing strips, using 2 ¼" decks screws or 8d ring-shank siding nails.
H. Building Paper
Building paper is installed on the roof decks as insurance in case leaks develop in shingles or flashing. It is sold in several weights, but 30# paper is a good choice to use under shingles. Lay the first course of building paper, overhanging the eaves by 3/8". Measure up from the eaves' edge to a point 32" above the top of the previous course of underlayment. Roll out the next course of building paper, always overlapping the first course by 4". Attach building paper with a hammer stapler, driving a staple every 6" to 12" at the edges and one staple per square foot in the field area. Install building paper up to the ridge - ruled side up - checking the alignment. Trim off the courses flush with the rake edge. Work your way up the roof deck with building paper courses, allowing 4" horizontal overlaps and 12" vertical seams. At valleys, roll building paper across from both sides, overlapping the ends by 36". Overlap hips and ridges by 6".
Fit building paper patches over obstructions like vent pipes and roof vents. Apply building paper up to the obstruction. Then resume laying the course on the opposite side, making sure to maintain the line. Cut a patch that overlaps the building paper by 12" on all sides. Make a cross-hatch cutout for the obstruction. Position the patch, staple it in place, then caulk the seams with roofing cement. At the bottom of dormers and sidewalls, tuck the building paper under the siding, where it intersects with the roof. Also tuck it under counterflashing on chimneys and skylights. Carefully pry up the siding and tuck at least 2" of paper under the siding. Leave the siding or counterflashing unfastened until after you install the step flashing. Attach the drip edge flashing along the rake edges.
I. To install Drip Edge Flashing
Drip edge flashing on the eaves is installed before the building paper is attached, while drip edge flashing at the rake edges is installed after building paper has been attached. To install drip edge flashing at the eaves, nail a strip of drip edge along the edge of the eaves. Overlap strips by 2" at vertical seams, and nail at 12" intervals. Miter the ends at a 45 degree angle to make a miter joint with the drip edge on the rake edge. Use galvanized roofing nails to install galvanized or vinyl drip edge; use aluminum nails for aluminum drip edge. Nail at 12" intervals. To install drip edge flashing at the rakes, start at the bottom, forming a miter joint with the drip edge at the eaves. Work toward the ridge, overlapping pieces of drip edge by 2". Make sure the higher strip is on top at the overlaps.
Flashing must be able to flex as the roof element and roof deck expand and contract. To bend flashing, first make a bending jig by driving screws into a piece of scrap wood, creating a space one-half the width of the flashing when measured from the edge of the board. Clamp the bending jig to a work surface. Lay a piece of flashing flat on the board, and bend it over the edge. Use old flashing as a template for making replacement pieces. This is very useful for reproducing complicated flashing, like saddle flashing for chimneys or dormers. If your roof originally had a cricket to divert water around the chimney, have a metalworker make a new one. Give the fabricator either the old cricket to use as a template, or the roof slope and chimney width to use as a guide.
J. To install Metal Valley Flashing
To install Metal Valley Flashing, start at the eaves. Set a piece of valley flashing into the valley, so the bottom of the "V" rests in the crease of the valley. Nail the flashing at 12" intervals along each side. Trim the end of the flashing at the eaves so it's flush with the drip edges at each side. Working toward the top, add flashing pieces, overlapping each at least 8", until you reach the ridge. Let the top piece of the flashing extend a few inches beyond the ridge. Bend the flashing over the ridge, so it lies flat on the opposite side of the roof. If you're installing preformed flashing, make a small cut in the spine for easier bending. Cover nail heads with roofing cement (unless you're using rubber-gasket nails). Also apply roofing cement along the side edges of the flashing.
K. To install Step Flashing
To install Step Flashing, shingle up to the element that requires flashing so the tops of the reveal areas are within 5" of the element. Install base flashing, using the old base flashing as a template. 
Bend a piece of step flashing in half and set it next to the lowest corner of the element.
Mark a trim line on the flashing, following the vertical edge of the element. Cut and remove the "waste" flashing. Pry out the lower courses of siding and any trim at the base of the element. Insert spacers to prop the trim or siding away from the work area.
Apply roofing cement to the base flashing in the area where the overlap with the step flashing will be formed. Tuck the trimmed piece of step flashing under the propped area, and secure the flashing. Fasten the flashing with one rubber-gasket nail driven near the top, and into the roof deck. Apply roofing cement to the top side of the first piece of step flashing, where it will be covered by the next shingle by pressing it firmly into the roofing cement. Don't nail through the flashing underneath. Tuck another piece of flashing under the trim or siding, overlapping the first piece of step flashing by at least 2". Set the flashing into roofing cement applied on the top of the shingle. Then nail the shingle in place, taking care not to drive nails through the flashing. Continue installing flashing in this manner up to the top of the element. Trim the last piece of the flashing to fit the top corner of the element. Reattach the siding and trim.
L. To install Chimney Flashing
To install Chimney Flashing, shingle up to the chimney base. Use the old base flashing as a template to cut new flashing. Bend up the counterflashing (pieces anchored in the chimney to cover the step flashing). Apply roofing cement to the base of the chimney and the shingles just below the base. Press the base flashing into the roofing cement and bend the flashing around the edges of the chimney. Drive rubber-gasket nails through the flashing flange into the roof deck. Install step flashing and shingles, working up the top of the chimney. Fasten flashing to the chimney with roofing cement. Fold down the counterflashing as you go. Cut and install top flashing (sometimes called a saddle) around the high side of the chimney, overlapping the final piece of flashing along each side, just as the base flashing was installed. Attach the flashing with roofing cement applied to the deck and the chimney, and with rubber-gasket nails driven through the base of the flashing and into the roof deck. Continue shingling past the chimney, using roofing cement (not nails) to attach shingles over the flashing.
